Evaluation of IR Biotyper for Lactiplantibacillus plantarum Typing and Its Application Potential in Probiotic Preliminary Screening

Abstract

IR Biotyper (IRBT), which is a spectroscopic system for microorganism typing based on Fourier transform infrared (FTIR) technology, has been used to detect the spread of clones in clinical microbiology laboratories. However, the use of IRBT to detect probiotics has rarely been reported. Herein, we evaluated the discriminatory power of IRBT to type Lactiplantibacillus plantarum isolates at the strain level and explored its application potential in probiotic preliminary selection. Twenty Lactiplantibacillus isolates collected from pickled radishes during successive fermentation were used to test the robustness of IRBT at the strain level. IRBT was then compared with genotyping methods such as whole-genome sequencing (WGS), pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST) to evaluate its discrimination power. IRBT distributed the 20 isolates into five clusters, with L. argentoratensis isolate C7-83 being the most distant from the other isolates, which belonged to L. plantarum. IRBT showed good reproducibility, although deviation in the discriminative power of IRBT was found at the strain level across laboratories, probably due to technical variance. All examined methods allowed bacterial identification at the strain level, but IRBT had higher discriminatory power than MLST and was comparable to the WGS and PFGE. In the phenotypic comparison study, we observed that the clustering results of probiotic physiological attributes (e.g., sensitivity to acid and bile salts, hydrophobicity of the cell surface, and resistance to antibiotics) were consistent with the typing results of IRBT. Our results indicated that IRBT is a robust tool for L. plantarum strain typing that could improve the efficiency of probiotic identification and preliminary screening, and can potentially be applied in probiotic traceability and quality control.

Performance Evaluation of the IR Biotyper® System for Clinical Microbiology: Application for Detection of Staphylococcus aureus Sequence Type 8 Strains

“…First, we spotted 12 μL instead of 15 μL of bacterial suspension from all three agar media onto silicon plates to reduce the amount of bacterial suspension. Second, the sample preparation sequence was changed from an EtOH-water method to a water-EtOH method [ 16 , 18 ]. Lastly, the amount of bacteria was reduced from a 1 μL loopful of bacterial culture to 0.5 μL loopful of bacterial culture.…”

“…In this regard, FTIR spectroscopy techniques could be an alternative for rapid and accurate strain typing. To date, Klebsiella pneumoniae , Acinetobacter baumannii , and Lactiplantibacillus plantarum have been evaluated for strain typing using the IRBT ® [ 16 , 18 , 26 ]. However, this method is challenging for S. aureus strain typing.…”

“…FTIR spectroscopy systems are known to be affected by features of bacterial colonies, which are affected by the culture media [ 18 ]. TSA medium was recommended for S. aureus isolates according to the manufacturer’s instructions.…”

Surveillance diagnostic algorithm using real-time PCR assay and strain typing method development to assist with the control of C. auris amid COVID-19 pandemic

“…Literature has shown extensive reports illustrating the discriminatory power among both Gram-positive and Gram-negative bacteria, particularly Listeria spp., Bacillus spp., Pseudomonas spp., Klebsiella spp., and Salmonella spp., both at the genus and species levels ( Quintelas et al., 2018 ; Hu et al, 2020 ; Rakovitsky et al, 2020 ; Cordovana et al, 2021 ; Mullie et al, 2022 ; Pascale et al, 2022 ; Wang-Wang et al, 2022 ). The IR Biotyper has proven to be an effective tool for microbial strain typing, specifically for those pathogens that are associated with nosocomial outbreaks within the hospital setting ( Deidda et al, 2021 ; Lombardo et al, 2021 ; Guerro-Lozano et al, 2022 ; Hadas et al, 2022 ; Li et al, 2022 ; Passaris et. al., 2022 ).…”

In-process real-time probiotic phenotypic strain identity tracking: The use of Fourier transform infrared spectroscopy

“…lactis , demonstrating to overcome some limitations of genomic-based methodologies and detecting phenotypic information that cannot be evidenced by DNA-based techniques. In addition, another work on discriminating Lactiplantibacillus plantarum strains demonstrated that FTIRS was not only comparable to WGS and PFGE but also had a higher discriminatory power than MLST ( Li et al, 2022 ). This complies with the fact that the identification of bacteria at the strain level, revealing genetic information evidenced by phenotypic characteristics, is becoming increasingly important in modern microbiology.…”